Spray a 12-cup cupcake pan with cooking spray and line with paper liners; set aside.
In a medium mixing bowl, whisk together flour, baking powder, baking soda, salt, cinnamon and nutmeg; set aside.
In a large mixing bowl, whisk together eggs, pumpkin puree, sugar, oil, and vanilla.
Slowly whisk in the flour mixture to the pumpkin mixture; stir until well combined.
Pour batter into prepared cups, filling each cup 3/4 full.
Bake for 30 to 35 minutes, or until a toothpick inserted in the center comes out clean.
Cool in pan 5 minutes; transfer cupcakes to a wire rack to cool completely.
Prepare the Frosting
Using an electric mixer, beat together cream cheese and butter on low speed until smooth.
Add in the maple syrup and vanilla; mix until thoroughly combined.
With the mixer on low, gradually add the powdered sugar and mix until smooth.
Assemble the Cupcakes
When the cupcakes are cool, take a cupcake corer, set it in the center of the cupcake and gently twist into the cupcake, about half-way through and take it out.
Attach a large plain tip to your pastry bag.
Fill the pastry bag with prepared frosting.
Insert the tip of the pastry bag inside the hole that you previously emptied and fill it.
Continue to frost the top of the cupcakes and decorate with pumpkin candies.